LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -43.138326 0.0000000) to (15.250465 43.138326 4.9479041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6185922 4.5405082 4.9479041 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.138326 0.0000000) to (15.250465 43.138326 4.9479041) create_atoms CPU = 0.001 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6185922 4.5405082 4.9479041 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -43.138326 0.0000000) to (15.250465 43.138326 4.9479041) create_atoms CPU = 0.001 seconds 306 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 23 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 606 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_677715648236_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2420.5428 0 -2420.5428 80630.958 36 0 -2485.2904 0 -2485.2904 1767.1145 Loop time of 0.772915 on 1 procs for 36 steps with 606 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2420.5428056582 -2485.28823475476 -2485.29039945137 Force two-norm initial, final = 142.48126 0.21151903 Force max component initial, final = 35.774376 0.032027802 Final line search alpha, max atom move = 1.0000000 0.032027802 Iterations, force evaluations = 36 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76256 | 0.76256 | 0.76256 | 0.0 | 98.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059314 | 0.0059314 | 0.0059314 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004422 | | | 0.57 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5074.00 ave 5074 max 5074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106020.0 ave 106020 max 106020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106020 Ave neighs/atom = 174.95050 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -2485.2904 0 -2485.2904 1767.1145 6510.2495 39 0 -2485.308 0 -2485.308 -1092.9136 6525.6478 Loop time of 0.0683875 on 1 procs for 3 steps with 606 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2485.29039945137 -2485.30802488918 -2485.30804058834 Force two-norm initial, final = 19.535881 0.26841906 Force max component initial, final = 17.658232 0.11817098 Final line search alpha, max atom move = 0.0028497400 0.00033675656 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06615 | 0.06615 | 0.06615 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045631 | 0.00045631 | 0.00045631 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001781 | | | 2.60 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105804.0 ave 105804 max 105804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105804 Ave neighs/atom = 174.59406 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2485.308 0 -2485.308 -1092.9136 Loop time of 3.125e-06 on 1 procs for 0 steps with 606 atoms 160.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.125e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105796.0 ave 105796 max 105796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105796 Ave neighs/atom = 174.58086 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.070 | 5.070 | 5.070 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2485.308 -2485.308 15.276098 86.276653 4.9512848 -1092.9136 -1092.9136 -16.739269 -3291.0348 29.033153 2.3197535 249.36557 Loop time of 3.186e-06 on 1 procs for 0 steps with 606 atoms 156.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 3.186e-06 | | |100.00 Nlocal: 606.000 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5050.00 ave 5050 max 5050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52898.0 ave 52898 max 52898 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105796.0 ave 105796 max 105796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105796 Ave neighs/atom = 174.58086 Neighbor list builds = 0 Dangerous builds = 0 606 -2485.30804058834 eV 2.31975345434364 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01